MolNFT v1 · #126431 · protein

X-ray structure of uridine phosphorylase from vibrio cholerae in complex with uridine at 1.03 a resolution

5M2T: “X-ray structure of uridine phosphorylase from vibrio cholerae in complex with uridine at 1.03 a resolution”. X-ray diffraction, 4 ligands (URI, NA, MG), 16 pockets (best druggability 0.76). MolNFT v1 #126431 on GenesisL1: 3D…

PDB: 5M2T
Type: protein
Length: 1,509 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uridine phosphorylase
EC: 2.4.2.3
UniProt: Q9K4U1
Ligands: URI, NA, MG, CL
Pockets: 16 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, F	Uridine phosphorylase (EC 2.4.2.3)	protein	251	34% helix, 29% strand	Q9K4U1
B, D, E	Uridine phosphorylase (EC 2.4.2.3)	protein	252	32% helix, 29% strand	Q9K4U1

Ligands and binding sites

URI · Uridine · ligand · 6 copies · chains A, B, C, D, E, F
NA · Sodium ion · metal · 3 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · chains D
CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
EDO · 1,2-ethanediol · additive · chains E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	186	0.76	0.92	36	URI, EDO
2	489	0.72	0.81	75	empty
3	392	0.72	0.83	49	URI, CL
4	250	0.71	0.86	43	URI, CL
5	423	0.71	0.82	52	URI, CL

Interfaces

12 interfaces between chains.

E–F · 2123 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 2046 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1938 Å² buried · 19 hydrogen bonds · protein-protein
A–F · 1086 Å² buried · 6 hydrogen bonds · protein-protein
D–E · 1076 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5M2T · X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine at… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9K4U1
Elsewhere: RCSB PDB 5M2T · PDBe 5M2T · UniProt Q9K4U1

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